Abstract: DNA methylation is a common epigenetic modification in eukaryotes and plays a crucial role in the evolution of many physiological and disease processes. Methylated DNA has become a type of key biomarker, and accurate quantification of the methylation levels is of great value for clinical management and basic scientific research. However, current results based on different platforms and different methods often have more significant differences in results, and this uncertainty poses a great potential for its application. In this paper, we summarize some typical detection methods for the locus-specific methylation analysis, especially highlighting the application of digital PCR in DNA methylation detection with high sensitivity and accuracy, and analyze the key factors affecting the result accuracy, and finally prospect the establishment of a standard evaluation system for quantifying methylated DNA.